Align serine racemase (EC 5.1.1.18) (characterized)
to candidate PP_3446 PP_3446 threonine deaminase
Query= BRENDA::O59791 (323 letters) >FitnessBrowser__Putida:PP_3446 Length = 530 Score = 193 bits (491), Expect = 7e-54 Identities = 111/318 (34%), Positives = 172/318 (54%), Gaps = 14/318 (4%) Query: 5 LVLPTYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNA 64 L P YD A +TP+ + ++ +V K E+ Q +FK RGA Sbjct: 36 LAAPVYD-----------LAIETPLQAAPALSAALGNQVLLKREDLQPTFSFKIRGAYTR 84 Query: 65 LSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVI 124 LS+L + QR+ GV+T S+GNHAQ +AL+A LG+ A I+MP P KV + GG V+ Sbjct: 85 LSRLTDVQRERGVITASAGNHAQGVALAASHLGMKATIVMPTTTPSLKVEGVRSRGGHVV 144 Query: 125 MYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELF-EEVGPLDALFVCLG 183 ++ A ++++ EG T +PP+D P V+AGQGT A E+ + G LDA+FV +G Sbjct: 145 LHGESFPHALTHALKLADSEGATFVPPFDDPDVIAGQGTVAMEILRQRPGALDAIFVPVG 204 Query: 184 GGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLG 243 GGGL++G A ++ P+ +V GVEP N Q + G V + T ADG +G Sbjct: 205 GGGLIAGIAAYVKYLRPDVKVIGVEPADSNCLQAAMAVGERVILPQVGTFADGVAVAQIG 264 Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAAR--AMKEKLKNK 301 + F + + VD+++TVS +EL +K + + EP+G L+ A + +E ++ + Sbjct: 265 AHCFELCRHFVDEVVTVSSDELCAAIKDIYDDTRSITEPSGALAVAGIKKYVAREGVQGQ 324 Query: 302 RIGIIISGGNVDIERYAH 319 + I SG NV+ +R H Sbjct: 325 TLVAIDSGANVNFDRLRH 342 Lambda K H 0.318 0.135 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 357 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 323 Length of database: 530 Length adjustment: 31 Effective length of query: 292 Effective length of database: 499 Effective search space: 145708 Effective search space used: 145708 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory